1Release Note
2
3After v3.2.7  (not yet released)
4  * Move to semantic versioning scheme (see https://semver.org/).
5    Release numbers are MAJOR.MINOR.PATCH where a new MAJOR release
6    number means backward incompatible changes were made, a new MINOR
7    number means backward compatible features were added, and a new
8    PATCH number means backward compatible bugfixes were made.  We may
9    or may not use transient suffixes like "-alpha", "-beta" and "-rcN"
10    as well at times.
11
12v3.2.7 (Feb 13 2019)
13  * Added lognormal and flat ordered dirichelet distributions as
14    alternatives to the gamma prior on site variation across sites.
15  * Added new, optional moves for the fossilized birth-death model.
16  * Added new, optional parsimony-guided moves for non-clock trees.
17  * Support for Beagle 3 added.
18  * Added support for FMA and AVX instructions in built-in likelihood
19    calculators for 4by4 nucleotide models.
20  * Added basic command line option support on Unix systems (-h,-i,-v)
21  * Various minor bug fixes.
22
23v3.2.6 (Nov 25 2015)
24  * Add invertebrate mt, Echinoderm and Euplotid codes [lset code=invermt].
25  * Fix a bug of updating brls in tree-stretch move.
26  * Correct the proposal ratio in the add/delete branch move.
27  * Add more coding options for restriction site chars.
28
29v3.2.5 (Apr 8 2015)
30  * Fix pdf in the coalescent prior.
31  * Fix a few issues when appending to the previous run.
32  * Improve the efficiency of moving ancestral fossils.
33  * Add lognormal rate variation among sites [lset rate=lnorm].
34  * Add parsimony-biased SPR and TBR proposals (for developers).
35  * Other minor bug fixes and improvements.
36
37v3.2.4 (Jan 27 2015)
38  * Correct the proposal ratio in the node slider move for non-clock tree.
39  * Fix reporting ancestral states under GTR+I+G model.
40  * Fix the sliding window in the move of updating omega in codon model.
41  * Fix the likelihood and proposal ratio of NaN in the multi-species
42    coalescent analysis.
43  * Correct screen output messages for a few commands.
44  * Fix the interaction of MrBayes with Beagle for the Windows executable.
45  * Fix prior pdf of relative rates (rate multipliers).
46
47v3.2.3 (Oct 22 2014)
48  * Correct the proposal ratio in the extending TBR move for non-clock tree.
49  * Fix numerical error of calculating proposal ratio in
50    parsimony-biased SPR moves.
51  * Set unconstrained:gammadir prior as default to help avoid
52    overestimating branch lengths.
53  * Add clock:fossilization prior for total-evidence dating analysis.
54  * Add LG model to Aamodelpr [prset aamodelpr=fixed(LG)].
55  * Rearrange the code to be more concise.
56  * Other minor bug fixes and improvements.
57
58v3.2.2 (Aug 22 2013)
59  * Disable LIKE_EPSILON warning for standard users.
60  * Fix segmentation fault errors in 64bit version.
61  * Fix some issues when dealing with constraints.
62  * Fix setting aarevmatpr parameters to fixed for GTR.
63  * Other bug fixes and improvements.
64
65v3.2.1 (Feb 8 2012)
66v3.2.0 (Nov 16 2011)
67  Major release.
68